The genome sequence of the Six-belted Clearwing, Bembecia ichneumoniformis (Denis & Schiffermüller, 1775)

We present a genome assembly from an individual male Bembecia ichneumoniformis (the Six-belted Clearwing; Arthropoda; Insecta; Lepidoptera; Sesiidae). The genome sequence is 511.4 megabases in span. Most of the assembly is scaffolded into 31 chromosomal pseudomolecules, including the Z sex chromosome. The mitochondrial genome has also been assembled and is 15.32 kilobases in length. Gene annotation of this assembly on Ensembl identified 12,114 protein coding genes.


Background
The Six-belted Clearwing (Bembecia ichneumoniformis) is a member of the Sesiidae family of clearwing moths.Thought to be Batesian mimics of Hymenoptera, Clearwing moths have narrow wings with transparent regions free of scales, and black bodies banded with red or yellow.The specific name ichneumoniformis means that its shape and colours, as well as the structure of its wings, evokes certain ichneumonids.Males of Bembecia ichneumoniformis exhibit six yellow bands across the abdomen, while females have five.In both sexes, there are orange scales at the tip and along the central bar of the forewings, with legs that are largely yellow (Waring et al., 2017).This species has been recorded in most of Europe and Asia Minor, the Caucasus, northern Iran and the Near East (GBIF Secretariat, 2023).In Britain and Ireland, the moth is classified as "Nationally Scarce B" (Butterfly Conservation, 2023), and is recorded mostly from England and Wales.The moth favours habitats such as chalk and coastal grasslands featuring grassy swards, as well as rough upland fields, embankments, quarries, and cliffs, avoiding areas with heavy grazing (Waring et al., 2017).
The caterpillars feed on specific plants including common bird's-foot-trefoil (Lotus corniculatus), kidney vetch (Anthyllis vulneraria), and possibly horseshoe vetch (Hippocrepis comosa).Indicators of larval presence, such as frass, may be found along the main root of the larval food plant (Waring et al., 2017).Adult specimens are often collected using sweep nets.The larval feeding period extends from July until the following May, and the species overwinters as larvae.The flight season occurs once a year, usually from late June to mid-August.During this period, males are particularly attracted to pheromone lures.
The genome of the six-belted clearwing, Bembecia ichneumoniformis, was sequenced as part of the Darwin Tree of Life Project, a collaborative effort to sequence all named eukaryotic species in the Atlantic Archipelago of Britain and Ireland.Here we present a chromosomally complete genome sequence for Bembecia ichneumoniformis, based on one male specimen from Wytham Woods, Oxfordshire, UK.

Genome sequence report
The genome was sequenced from one male Bembecia ichneumoniformis (Figure 1) collected from Wytham Woods, Oxfordshire, UK (51.77,.A total of 30-fold coverage in Pacific Biosciences single-molecule HiFi long reads and 93-fold coverage in 10X Genomics read clouds were generated.Primary assembly contigs were scaffolded with chromosome conformation Hi-C data.Manual assembly curation corrected 33 missing joins or mis-joins and removed one haplotypic duplication, reducing the scaffold number by 32.76% and increasing the scaffold N50 by 6.43%. The final assembly has a total length of 511.4 Mb in 38 sequence scaffolds with a scaffold N50 of 18.8 Mb (Table 1).A summary of the assembly statistics is shown in Figure 2, while the distribution of assembly scaffolds on GC proportion and coverage is shown in Figure 3.The cumulative assembly plot in Figure 4 shows curves for subsets of scaffolds assigned to different phyla.Most (99.95%) of the assembly sequence was assigned to 31 chromosomal-level scaffolds, representing 30 autosomes and the Z sex chromosome.Chromosome-scale scaffolds confirmed by the Hi-C data are named in order of size (Figure 5; Table 2).While not fully phased, the assembly deposited is of one haplotype.Contigs corresponding to the second haplotype have also been deposited.The mitochondrial genome was also assembled and can be found as a contig within the multifasta file of the genome submission.
Metadata for specimens, barcode results, spectra estimates, sequencing runs, contaminants and pre-curation assembly statistics can be found at https://links.tol.sanger.ac.uk/ species/301037.

Sample acquisition and nucleic acid extraction
A male Bembecia ichneumoniformis (specimen ID Ox000506, individual ilBemIchn1) was collected from Wytham Woods, Oxfordshire (biological vice-county Berkshire), UK (latitude 51.77, longitude -1.33) on 2020-06-23, using an API pheromone lure.The specimen was collected and identified by Douglas Boyes (University of Oxford) and preserved on dry ice.
DNA was extracted at the Tree of Life laboratory, Wellcome Sanger Institute (WSI).The ilBemIchn1 sample was weighed and dissected on dry ice with tissue set aside for Hi-C sequencing.Tissue from the abdomen disrupted using a Nippi Powermasher fitted with a BioMasher pestle.High molecular weight (HMW) DNA was extracted using the Qiagen MagAttract HMW DNA extraction kit.Low molecular weight DNA was removed from a 20 ng aliquot of extracted DNA using the 0.8X AMpure XP purification kit prior to 10X Chromium sequencing; a minimum of 50 ng DNA was submitted for 10X sequencing.HMW DNA was sheared into an average fragment size of 12-20 kb in a Megaruptor 3 system with speed setting 30.Sheared DNA was purified by solid-phase reversible immobilisation using AMPure PB beads with a 1.8X ratio of beads to sample to remove the shorter fragments and concentrate the DNA sample.The concentration    et al., 2020) or MITOS (Bernt et al., 2013) and uses these annotations to select the final mitochondrial contig and to ensure the general quality of the sequence.
Table 3 contains a list of relevant software tool versions and sources.

Genome annotation
The Ensembl gene annotation system (Aken et al., 2016) was used to generate annotation for the Bembecia ichneumoniformis assembly (GCA_910589475.1).Annotation was created primarily through alignment of transcriptomic data to the genome, with gap filling via protein-to-genome alignments of a select set of proteins from UniProt (UniProt Consortium, 2019).

Wellcome Sanger Institute -Legal and Governance
The materials that have contributed to this genome note have been supplied by a Darwin Tree of Life Partner.The submission of materials by a Darwin Tree of Life Partner is subject to the 'Darwin Tree of Life Project Sampling Code of Practice', which can be found in full on the Darwin Tree of Life website here.By agreeing with and signing up to the Sampling Code of Practice, the Darwin Tree of Life Partner agrees they will meet the legal and ethical requirements and standards set out within this document in respect of all samples acquired for, and supplied to, the Darwin Tree of Life Project.
Further, the Wellcome Sanger Institute employs a process whereby due diligence is carried out proportionate to the nature of the materials themselves, and the circumstances under which they have been/are to be collected and provided for  Table 3. Software tools: versions and sources.

Software tool Version
use.The purpose of this is to address and mitigate any potential legal and/or ethical implications of receipt and use of the materials as part of the research project, and to ensure that in doing so we align with best practice wherever possible.The overarching areas of consideration are: • Ethical review of provenance and sourcing of the material

Paul R Johnston
University of St Andrews, St Andrews, Scotland, UK There is really not much at all to add to this.The report is presented in the standard tree of life format and all data and metadata seem to be present in the relevant databases and are appropriately linked.The methods are presented in sufficient detail and a detailed protocol is linked.
Is the rationale for creating the dataset(s) clearly described?

Wenfeng Chen
Fuzhou University, Fuzhou, Fujian, China The article focuses on the creation and presentation of Bembecia ichneumoniformis genome datasets.It outlines the rationale for creating these datasets, provides detailed information on the methods and materials used in their creation, and describes how the dataset is presented in a usable and accessible format for genomic research.
Rationale for Creating the Dataset: The article clearly states the scientific or practical reasons for generating these genome datasets.This includes explaining the research questions, the significance of the genomic data, and how the datasets contribute to understanding genetic aspects of the studied organism or phenomenon.

Details of Methods and Materials:
The article includes comprehensive details of the genome sequencing or analysis methods, data sources (e.g., sequencing platforms, software tools), quality control procedures, and any genomic variations or annotations considered.This ensures the reproducibility and reliability of the dataset creation process.

Presentation of Datasets:
The dataset is organized in a structured format suitable for genomic analysis.Each dataset is well-documented with metadata describing the genome assembly, annotation, genetic variants, and relevant genomic features.Providing open-access formats and repositories facilitates accessibility and use by other researchers.

Is the rationale for creating the dataset(s) clearly described? Yes
Are the protocols appropriate and is the work technically sound?Yes

Are sufficient details of methods and materials provided to allow replication by others? Yes
Are the datasets clearly presented in a useable and accessible format?Yes Competing Interests: No competing interests were disclosed.

Reviewer Expertise: Insect Genetics and Neuroscience
I confirm that I have read this submission and believe that I have an appropriate level of expertise to confirm that it is of an acceptable scientific standard.

Figure 2 .
Figure 2. Genome assembly of Bembecia ichneumoniformis, ilBemIchn1.2:metrics.The BlobToolKit Snailplot shows N50 metrics and BUSCO gene completeness.The main plot is divided into 1,000 size-ordered bins around the circumference with each bin representing 0.1% of the 511,410,357 bp assembly.The distribution of scaffold lengths is shown in dark grey with the plot radius scaled to the longest scaffold present in the assembly (22,154,014 bp, shown in red).Orange and pale-orange arcs show the N50 and N90 scaffold lengths (18,823,830 and 12,162,325 bp), respectively.The pale grey spiral shows the cumulative scaffold count on a log scale with white scale lines showing successive orders of magnitude.The blue and pale-blue area around the outside of the plot shows the distribution of GC, AT and N percentages in the same bins as the inner plot.A summary of complete, fragmented, duplicated and missing BUSCO genes in the lepidoptera_odb10 set is shown in the top right.An interactive version of this figure is available at https://blobtoolkit.genomehubs.org/view/ilBemIchn1.2/dataset/CAJUUH02/snail.

Figure 5 .
Figure 5. Genome assembly of Bembecia ichneumoniformis, ilBemIchn1.2:Hi-C contact map of the ilBemIchn1.2assembly, visualised using HiGlass.Chromosomes are shown in order of size from left to right and top to bottom.An interactive version of this figure may be viewed at https://genome-note-higlass.tol.sanger.ac.uk/l/?d=CTGaP8xaT7CnLlRJWDRwrg.

Yes Are the protocols appropriate and is the work technically sound? Yes Are sufficient details of methods and materials provided to allow replication by others? Yes Are the datasets clearly presented in a useable and accessible format? Yes Competing Interests:
No competing interests were disclosed.

have read this submission and believe that I have an appropriate level of expertise to confirm that it is of an acceptable scientific standard.
This is an open access peer review report distributed under the terms of the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited.